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Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human.

Gupta VK, Chaudhari NM, Iskepalli S, Dutta C - BMC Genomics (2015)

Bottom Line: Distribution of various functional COG categories differs significantly among the habitat-specific genes.Prevotella genomes derived from different body sites differ appreciably in gene repertoire, suggesting that these microbiome components might have developed distinct genetic strategies for niche adaptation within the host.Each individual microbe might also have a component of its own genetic machinery for host adaptation, as appeared from the huge number of singletons.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology & Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032, India. vinodgupta299@gmail.com.

ABSTRACT

Background: The community composition of the human microbiome is known to vary at distinct anatomical niches. But little is known about the nature of variations, if any, at the genome/sub-genome levels of a specific microbial community across different niches. The present report aims to explore, as a case study, the variations in gene repertoire of 28 Prevotella reference genomes derived from different body-sites of human, as reported earlier by the Human Microbiome Consortium.

Results: The pan-genome for Prevotella remains "open". On an average, 17% of predicted protein-coding genes of any particular Prevotella genome represent the conserved core genes, while the remaining 83% contribute to the flexible and singletons. The study reveals exclusive presence of 11798, 3673, 3348 and 934 gene families and exclusive absence of 17, 221, 115 and 645 gene families in Prevotella genomes derived from human oral cavity, gastro-intestinal tracts (GIT), urogenital tract (UGT) and skin, respectively. Distribution of various functional COG categories differs significantly among the habitat-specific genes. No niche-specific variations could be observed in distribution of KEGG pathways.

Conclusions: Prevotella genomes derived from different body sites differ appreciably in gene repertoire, suggesting that these microbiome components might have developed distinct genetic strategies for niche adaptation within the host. Each individual microbe might also have a component of its own genetic machinery for host adaptation, as appeared from the huge number of singletons.

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COG frequency heatmap. All coding genes annotated against COG database and frequencies of functional COG categories were hierarchically clustered in two dimensions. The horizontal axis shows the percentage frequency of genes involved in respective functional COG category, while the strains are located on vertical axis.
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Fig5: COG frequency heatmap. All coding genes annotated against COG database and frequencies of functional COG categories were hierarchically clustered in two dimensions. The horizontal axis shows the percentage frequency of genes involved in respective functional COG category, while the strains are located on vertical axis.

Mentions: Realization of the fact that the lineage-specific selections and niche-specific constraints both might have played significant roles in shaping the genomic architectures of the microbiome components under study has prompted us to examine the distribution of KEGG pathways and major COG categories in 28 Prevotella genomes and 3 Bacteroides genomes of the current dataset. Clusters of 31 genomes generated on the basis of the distribution of major KEGG pathway categories and COG categories have been shown along with their heat-maps in FigureĀ 4 and 5, respectively.Figure 4


Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human.

Gupta VK, Chaudhari NM, Iskepalli S, Dutta C - BMC Genomics (2015)

COG frequency heatmap. All coding genes annotated against COG database and frequencies of functional COG categories were hierarchically clustered in two dimensions. The horizontal axis shows the percentage frequency of genes involved in respective functional COG category, while the strains are located on vertical axis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4359502&req=5

Fig5: COG frequency heatmap. All coding genes annotated against COG database and frequencies of functional COG categories were hierarchically clustered in two dimensions. The horizontal axis shows the percentage frequency of genes involved in respective functional COG category, while the strains are located on vertical axis.
Mentions: Realization of the fact that the lineage-specific selections and niche-specific constraints both might have played significant roles in shaping the genomic architectures of the microbiome components under study has prompted us to examine the distribution of KEGG pathways and major COG categories in 28 Prevotella genomes and 3 Bacteroides genomes of the current dataset. Clusters of 31 genomes generated on the basis of the distribution of major KEGG pathway categories and COG categories have been shown along with their heat-maps in FigureĀ 4 and 5, respectively.Figure 4

Bottom Line: Distribution of various functional COG categories differs significantly among the habitat-specific genes.Prevotella genomes derived from different body sites differ appreciably in gene repertoire, suggesting that these microbiome components might have developed distinct genetic strategies for niche adaptation within the host.Each individual microbe might also have a component of its own genetic machinery for host adaptation, as appeared from the huge number of singletons.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology & Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032, India. vinodgupta299@gmail.com.

ABSTRACT

Background: The community composition of the human microbiome is known to vary at distinct anatomical niches. But little is known about the nature of variations, if any, at the genome/sub-genome levels of a specific microbial community across different niches. The present report aims to explore, as a case study, the variations in gene repertoire of 28 Prevotella reference genomes derived from different body-sites of human, as reported earlier by the Human Microbiome Consortium.

Results: The pan-genome for Prevotella remains "open". On an average, 17% of predicted protein-coding genes of any particular Prevotella genome represent the conserved core genes, while the remaining 83% contribute to the flexible and singletons. The study reveals exclusive presence of 11798, 3673, 3348 and 934 gene families and exclusive absence of 17, 221, 115 and 645 gene families in Prevotella genomes derived from human oral cavity, gastro-intestinal tracts (GIT), urogenital tract (UGT) and skin, respectively. Distribution of various functional COG categories differs significantly among the habitat-specific genes. No niche-specific variations could be observed in distribution of KEGG pathways.

Conclusions: Prevotella genomes derived from different body sites differ appreciably in gene repertoire, suggesting that these microbiome components might have developed distinct genetic strategies for niche adaptation within the host. Each individual microbe might also have a component of its own genetic machinery for host adaptation, as appeared from the huge number of singletons.

Show MeSH
Related in: MedlinePlus